Contacts of the strand formed by residues 363 - 371 (chain B) in PDB entry 5YL4


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with MET 363 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272B  PRO*     3.8    10.7    -      -       -      +
    283B  ALA*     4.5    12.4    -      -       +      +
    284B  LEU*     3.5    33.0    +      -       -      +
    285B  THR*     4.8     0.2    -      -       -      -
    286B  VAL*     3.8    31.6    -      -       +      +
    289B  LEU*     3.7    27.1    -      -       +      +
    318B  ARG      3.2    15.5    -      -       -      +
    319B  GLY*     4.3     2.0    -      -       -      -
    320B  ARG      4.2     9.9    -      -       -      +
    321B  MET*     3.8    23.1    -      -       +      -
    357B  PRO*     5.1     1.1    -      -       -      -
    358B  PRO*     5.6     0.2    -      -       -      -
    361B  LEU*     3.3     6.2    -      -       -      +
    362B  LYS*     1.3    85.4    -      -       +      +
    364B  SER*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 364 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270B  PHE*     3.7    21.4    -      -       -      -
    271B  ALA      3.2    13.7    -      -       -      -
    272B  PRO*     4.2     4.0    -      -       -      -
    289B  LEU*     3.8     8.9    -      -       -      +
    317B  PHE*     3.5     1.9    -      -       -      -
    318B  ARG*     2.8    40.4    +      -       -      +
    358B  PRO*     3.4    29.7    -      -       -      +
    361B  LEU*     4.3     4.0    -      -       -      -
    363B  MET*     1.3    74.7    -      -       -      +
    365B  ALA*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 365 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270B  PHE*     3.4     5.8    -      -       -      -
    271B  ALA*     2.8    38.2    +      -       +      +
    289B  LEU*     4.1    12.8    -      -       +      +
    293B  MET*     3.4    31.5    -      -       +      +
    316B  ILE      3.6     5.8    -      -       -      -
    317B  PHE*     3.8    19.7    -      -       +      -
    364B  SER*     1.3    78.5    -      -       -      +
    366B  THR*     1.3    62.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 366 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232B  THR*     4.1    13.0    -      -       +      +
    235B  GLY*     3.0    42.3    -      -       -      -
    236B  VAL*     4.0    18.4    -      -       +      +
    269B  GLY      3.5    11.2    -      -       -      +
    270B  PHE*     3.3    17.0    -      -       -      -
    293B  MET*     3.2     6.9    -      -       -      +
    315B  ALA*     3.4     2.8    -      -       -      -
    316B  ILE*     3.0    39.7    +      -       +      +
    318B  ARG*     5.6     2.6    -      -       -      +
    365B  ALA*     1.3    69.9    -      -       -      +
    367B  PHE*     1.3    64.6    +      -       -      +
    368B  ILE*     4.2     2.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 367 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267B  MET*     3.6    13.0    -      -       +      -
    268B  PRO*     3.4     6.4    -      -       -      +
    269B  GLY*     2.8    46.6    +      -       -      +
    293B  MET*     3.6    43.5    -      -       +      +
    294B  PHE*     3.7    21.1    -      +       -      -
    299B  MET*     3.9    20.4    -      -       +      -
    310B  TYR*     3.4    33.4    -      +       -      -
    313B  VAL*     3.4    25.1    -      -       +      -
    314B  ALA      3.9     2.5    -      -       -      -
    315B  ALA*     5.2     0.7    -      -       +      -
    366B  THR*     1.3    74.0    -      -       -      +
    368B  ILE*     1.3    62.5    +      -       -      +
    369B  GLY*     3.6    21.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 368 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200B  TYR*     3.7    13.0    -      -       +      +
    236B  VAL*     3.6    27.6    -      -       +      -
    257B  MET*     3.7    14.5    -      -       +      +
    266B  PHE*     3.6    33.2    -      -       +      -
    267B  MET      4.2     1.6    -      -       -      -
    268B  PRO*     4.9     1.6    -      -       +      -
    313B  VAL*     3.5     4.2    -      -       -      +
    314B  ALA*     2.9    42.4    +      -       +      +
    316B  ILE*     4.9     4.9    -      -       +      -
    366B  THR*     4.8     4.0    -      -       +      +
    367B  PHE*     1.3    78.9    -      -       -      +
    369B  GLY*     1.3    58.8    +      -       -      +
    506B  8WR      3.4    46.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 369 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  PHE*     3.3     5.0    -      -       -      -
    267B  MET*     2.7    46.7    +      -       -      +
    310B  TYR*     4.2     6.5    -      -       -      -
    312B  THR      4.1     3.8    -      -       -      -
    313B  VAL*     4.8     0.4    -      -       -      -
    367B  PHE*     3.6    22.8    -      -       -      -
    368B  ILE*     1.3    73.5    -      -       -      +
    370B  ASN*     1.3    60.9    +      -       -      -
    371B  SER      3.5     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 370 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257B  MET*     3.0    23.2    +      -       +      +
    258B  VAL*     4.4     0.4    -      -       -      +
    259B  PRO*     4.0     8.7    -      -       -      +
    263B  LEU      3.3    25.5    +      -       -      +
    265B  PHE      4.4     6.2    -      -       -      +
    266B  PHE*     3.5    27.0    -      -       +      -
    310B  TYR*     3.8     1.1    -      -       -      -
    311B  LEU*     2.8    43.1    +      -       -      +
    312B  THR*     3.1    27.3    +      -       -      +
    368B  ILE      4.1     1.2    +      -       -      -
    369B  GLY*     1.3    69.8    -      -       -      -
    371B  SER*     1.3    61.1    +      -       -      +
    422B  TYR*     4.8     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 371 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265B  PHE      4.8     1.6    +      -       -      +
    267B  MET*     3.9    19.9    -      -       -      +
    305B  PRO*     4.6     4.6    +      -       -      +
    308B  GLY      4.4     1.0    -      -       -      -
    309B  ARG      3.6    14.8    +      -       -      -
    310B  TYR*     3.8    25.5    -      -       -      -
    311B  LEU*     5.2     0.4    -      -       -      -
    369B  GLY      3.5     3.8    +      -       -      -
    370B  ASN*     1.3    78.6    -      -       -      +
    372B  THR*     1.3    64.7    +      -       -      +
    373B  ALA*     3.0    21.2    +      -       -      +
    374B  ILE*     3.3    23.9    +      -       -      +
    422B  TYR*     4.2     3.0    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il